Starting phenix.real_space_refine on Thu Jul 2 20:53:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vb3_64914/07_2026/9vb3_64914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vb3_64914/07_2026/9vb3_64914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vb3_64914/07_2026/9vb3_64914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vb3_64914/07_2026/9vb3_64914.map" model { file = "/net/cci-nas-00/data/ceres_data/9vb3_64914/07_2026/9vb3_64914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vb3_64914/07_2026/9vb3_64914.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.009 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 6458 2.51 5 N 1742 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10182 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2537 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 311} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2810 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 346} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2588 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.21 Number of scatterers: 10182 At special positions: 0 Unit cell: (103.75, 121.733, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 2 15.00 O 1914 8.00 N 1742 7.00 C 6458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.01 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.16 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 377.7 milliseconds 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 40.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 59 through 89 Processing helix chain 'R' and resid 101 through 119 removed outlier: 3.571A pdb=" N LEU R 105 " --> pdb=" O VAL R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 128 removed outlier: 3.653A pdb=" N ILE R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 172 Processing helix chain 'R' and resid 172 through 180 removed outlier: 4.081A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 206 removed outlier: 3.932A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Proline residue: R 202 - end of helix Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 273 Processing helix chain 'R' and resid 294 through 329 removed outlier: 3.605A pdb=" N ARG R 299 " --> pdb=" O VAL R 295 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG R 306 " --> pdb=" O VAL R 302 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 365 removed outlier: 3.618A pdb=" N TYR R 339 " --> pdb=" O THR R 335 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP R 340 " --> pdb=" O PRO R 336 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 370 through 375 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.504A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.788A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 92 removed outlier: 3.673A pdb=" N GLN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 117 Processing helix chain 'A' and resid 120 through 134 removed outlier: 3.798A pdb=" N SER A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.840A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.909A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.603A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.777A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 347 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.726A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.553A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.614A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 7.057A pdb=" N LEU A 39 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE A 222 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.330A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.612A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.944A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.670A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.577A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 232 removed outlier: 3.798A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.560A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.684A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.143A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1677 1.31 - 1.44: 2868 1.44 - 1.57: 5730 1.57 - 1.70: 20 1.70 - 1.82: 99 Bond restraints: 10394 Sorted by residual: bond pdb=" CG LEU R 118 " pdb=" CD1 LEU R 118 " ideal model delta sigma weight residual 1.521 1.248 0.273 3.30e-02 9.18e+02 6.86e+01 bond pdb=" CA SER R 330 " pdb=" CB SER R 330 " ideal model delta sigma weight residual 1.528 1.429 0.099 1.48e-02 4.57e+03 4.46e+01 bond pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta sigma weight residual 1.528 1.428 0.100 1.61e-02 3.86e+03 3.84e+01 bond pdb=" CG LEU R 118 " pdb=" CD2 LEU R 118 " ideal model delta sigma weight residual 1.521 1.722 -0.201 3.30e-02 9.18e+02 3.71e+01 bond pdb=" C5 GDP A 401 " pdb=" C4 GDP A 401 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 ... (remaining 10389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.65: 13153 4.65 - 9.30: 863 9.30 - 13.94: 69 13.94 - 18.59: 5 18.59 - 23.24: 2 Bond angle restraints: 14092 Sorted by residual: angle pdb=" C ASP B 291 " pdb=" CA ASP B 291 " pdb=" CB ASP B 291 " ideal model delta sigma weight residual 110.36 87.12 23.24 1.85e+00 2.92e-01 1.58e+02 angle pdb=" CB GLU D 234 " pdb=" CG GLU D 234 " pdb=" CD GLU D 234 " ideal model delta sigma weight residual 112.60 133.52 -20.92 1.70e+00 3.46e-01 1.51e+02 angle pdb=" N VAL D 127 " pdb=" CA VAL D 127 " pdb=" CB VAL D 127 " ideal model delta sigma weight residual 110.82 123.48 -12.66 1.11e+00 8.12e-01 1.30e+02 angle pdb=" CA ASP B 291 " pdb=" CB ASP B 291 " pdb=" CG ASP B 291 " ideal model delta sigma weight residual 112.60 123.14 -10.54 1.00e+00 1.00e+00 1.11e+02 angle pdb=" CA ASP B 163 " pdb=" CB ASP B 163 " pdb=" CG ASP B 163 " ideal model delta sigma weight residual 112.60 121.47 -8.87 1.00e+00 1.00e+00 7.86e+01 ... (remaining 14087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.41: 5429 20.41 - 40.83: 556 40.83 - 61.24: 147 61.24 - 81.65: 28 81.65 - 102.06: 10 Dihedral angle restraints: 6170 sinusoidal: 2384 harmonic: 3786 Sorted by residual: dihedral pdb=" C ASP B 291 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" CB ASP B 291 " ideal model delta harmonic sigma weight residual -122.60 -97.44 -25.16 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -169.20 83.20 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 170.00 -77.00 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 6167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 1172 0.159 - 0.318: 374 0.318 - 0.478: 41 0.478 - 0.637: 9 0.637 - 0.796: 2 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CA GLU A 8 " pdb=" N GLU A 8 " pdb=" C GLU A 8 " pdb=" CB GLU A 8 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" CG LEU R 71 " pdb=" CB LEU R 71 " pdb=" CD1 LEU R 71 " pdb=" CD2 LEU R 71 " both_signs ideal model delta sigma weight residual False -2.59 -3.31 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA SER R 330 " pdb=" N SER R 330 " pdb=" C SER R 330 " pdb=" CB SER R 330 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.92e+00 ... (remaining 1595 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 49 " 0.748 9.50e-02 1.11e+02 3.45e-01 1.50e+02 pdb=" NE ARG B 49 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 49 " -0.165 2.00e-02 2.50e+03 pdb=" NH1 ARG B 49 " 0.048 2.00e-02 2.50e+03 pdb=" NH2 ARG B 49 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 142 " -0.560 9.50e-02 1.11e+02 2.64e-01 1.26e+02 pdb=" NE ARG A 142 " 0.092 2.00e-02 2.50e+03 pdb=" CZ ARG A 142 " -0.155 2.00e-02 2.50e+03 pdb=" NH1 ARG A 142 " 0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 142 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 67 " -0.602 9.50e-02 1.11e+02 2.78e-01 1.03e+02 pdb=" NE ARG D 67 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 67 " 0.139 2.00e-02 2.50e+03 pdb=" NH1 ARG D 67 " -0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG D 67 " -0.062 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1158 2.79 - 3.32: 10527 3.32 - 3.85: 16409 3.85 - 4.37: 21122 4.37 - 4.90: 34696 Nonbonded interactions: 83912 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.268 3.040 nonbonded pdb=" O ASP B 291 " pdb=" CB ASP B 291 " model vdw 2.310 2.752 nonbonded pdb=" OG SER R 213 " pdb=" O ASP R 215 " model vdw 2.379 3.040 nonbonded pdb=" O LEU A 156 " pdb=" N LEU A 159 " model vdw 2.386 3.120 nonbonded pdb=" O ASP D 211 " pdb=" OH TYR D 215 " model vdw 2.406 3.040 ... (remaining 83907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.273 10397 Z= 0.853 Angle : 2.591 23.241 14098 Z= 1.731 Chirality : 0.151 0.796 1598 Planarity : 0.025 0.345 1785 Dihedral : 18.250 102.059 3721 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 7.69 % Allowed : 17.20 % Favored : 75.11 % Cbeta Deviations : 4.34 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.20), residues: 1285 helix: -2.21 (0.20), residues: 481 sheet: -1.47 (0.34), residues: 220 loop : -2.38 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.161 0.016 ARG A 142 TYR 0.084 0.010 TYR A 167 PHE 0.058 0.010 PHE C 61 TRP 0.062 0.013 TRP B 99 HIS 0.036 0.008 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01403 / 0.85 (10394) covalent geometry : angle 2.58699 / 1.73 (14092) SS BOND : bond 0.07685 / 5.44 ( 3) SS BOND : angle 7.40485 / 4.35 ( 6) hydrogen bonds : bond 0.22657 / 15.98 ( 504) hydrogen bonds : angle 8.98143 / 6.49 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 258 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 55 ASP cc_start: 0.9068 (m-30) cc_final: 0.8828 (p0) REVERT: R 63 LYS cc_start: 0.9418 (mtmm) cc_final: 0.9167 (mtmt) REVERT: R 94 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8550 (mt) REVERT: R 120 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8184 (tpp) REVERT: R 134 TRP cc_start: 0.8716 (t-100) cc_final: 0.7782 (t-100) REVERT: R 187 LYS cc_start: 0.8895 (mtpm) cc_final: 0.8534 (tmtt) REVERT: R 292 PRO cc_start: 0.7108 (Cg_exo) cc_final: 0.6846 (Cg_endo) REVERT: R 306 ARG cc_start: 0.8702 (mmt180) cc_final: 0.8479 (mmm-85) REVERT: R 333 GLN cc_start: 0.7752 (tt0) cc_final: 0.7525 (tp40) REVERT: R 350 ASN cc_start: 0.9132 (m-40) cc_final: 0.8866 (m110) REVERT: A 25 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8741 (tm-30) REVERT: A 43 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.9005 (mm-30) REVERT: A 66 CYS cc_start: 0.9385 (m) cc_final: 0.8801 (m) REVERT: A 108 PHE cc_start: 0.9204 (m-80) cc_final: 0.8977 (m-80) REVERT: A 128 LYS cc_start: 0.9721 (ttpp) cc_final: 0.9495 (mmtt) REVERT: A 142 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8194 (mtm-85) REVERT: A 145 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8746 (pm20) REVERT: A 171 GLN cc_start: 0.8732 (mt0) cc_final: 0.8098 (mm-40) REVERT: A 248 LYS cc_start: 0.9662 (OUTLIER) cc_final: 0.9448 (ttmm) REVERT: B 32 GLN cc_start: 0.9509 (mt0) cc_final: 0.9207 (mt0) REVERT: B 42 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8373 (ptm-80) REVERT: B 142 HIS cc_start: 0.8937 (OUTLIER) cc_final: 0.7871 (m170) REVERT: C 22 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8698 (mt-10) REVERT: C 31 SER cc_start: 0.9648 (t) cc_final: 0.9361 (p) REVERT: D 73 ASP cc_start: 0.9145 (t0) cc_final: 0.8494 (t0) REVERT: D 76 LYS cc_start: 0.9499 (mppt) cc_final: 0.9169 (mttp) REVERT: D 109 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8805 (p0) REVERT: D 128 MET cc_start: 0.9035 (mmm) cc_final: 0.8688 (mmm) REVERT: D 206 ARG cc_start: 0.9170 (ptp-110) cc_final: 0.8938 (ttp80) outliers start: 84 outliers final: 27 residues processed: 317 average time/residue: 0.1117 time to fit residues: 47.3132 Evaluate side-chains 218 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 238 GLN R 261 ASN R 343 HIS R 350 ASN R 370 ASN R 373 HIS A 106 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN B 6 GLN B 91 HIS B 142 HIS B 259 GLN B 266 HIS B 311 HIS C 44 HIS D 39 GLN D 130 GLN D 219 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.069092 restraints weight = 19751.026| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.92 r_work: 0.2767 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10397 Z= 0.150 Angle : 0.694 7.370 14098 Z= 0.368 Chirality : 0.045 0.217 1598 Planarity : 0.005 0.064 1785 Dihedral : 10.334 132.695 1500 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.76 % Allowed : 21.23 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.22), residues: 1285 helix: 0.63 (0.22), residues: 477 sheet: -1.01 (0.30), residues: 274 loop : -1.61 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 90 TYR 0.019 0.002 TYR R 339 PHE 0.016 0.002 PHE A 336 TRP 0.022 0.002 TRP B 82 HIS 0.008 0.001 HIS R 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (10394) covalent geometry : angle 0.69359 / 0.37 (14092) SS BOND : bond 0.00532 / 0.37 ( 3) SS BOND : angle 1.43136 / 0.97 ( 6) hydrogen bonds : bond 0.05479 / 3.77 ( 504) hydrogen bonds : angle 5.51835 / 4.05 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 55 ASP cc_start: 0.8636 (m-30) cc_final: 0.8287 (p0) REVERT: R 57 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8724 (p0) REVERT: R 59 ASP cc_start: 0.7542 (t0) cc_final: 0.7245 (t0) REVERT: R 63 LYS cc_start: 0.9314 (mtmm) cc_final: 0.9055 (mtmt) REVERT: R 94 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8519 (mt) REVERT: R 120 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7696 (tpp) REVERT: R 123 GLU cc_start: 0.9152 (tt0) cc_final: 0.8927 (tt0) REVERT: R 134 TRP cc_start: 0.8405 (t-100) cc_final: 0.7015 (t-100) REVERT: R 171 CYS cc_start: 0.8964 (m) cc_final: 0.8637 (m) REVERT: R 262 LYS cc_start: 0.7954 (tppt) cc_final: 0.7663 (tptp) REVERT: R 268 ARG cc_start: 0.8682 (mtp-110) cc_final: 0.8465 (mtm110) REVERT: R 350 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8757 (m-40) REVERT: R 365 ASN cc_start: 0.7845 (t0) cc_final: 0.7629 (t0) REVERT: A 43 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8717 (mm-30) REVERT: A 84 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9019 (tt) REVERT: A 88 MET cc_start: 0.8335 (ttt) cc_final: 0.8013 (ptm) REVERT: A 123 LEU cc_start: 0.9422 (mt) cc_final: 0.9143 (mm) REVERT: A 321 THR cc_start: 0.9370 (m) cc_final: 0.8864 (p) REVERT: B 42 ARG cc_start: 0.8368 (ttt-90) cc_final: 0.7448 (ttp-170) REVERT: B 44 GLN cc_start: 0.8633 (tp40) cc_final: 0.8368 (pm20) REVERT: B 59 TYR cc_start: 0.9145 (m-80) cc_final: 0.8648 (m-80) REVERT: B 130 GLU cc_start: 0.8949 (mp0) cc_final: 0.8703 (mp0) REVERT: B 188 MET cc_start: 0.8910 (mmm) cc_final: 0.8603 (mmm) REVERT: B 189 SER cc_start: 0.9142 (t) cc_final: 0.8842 (m) REVERT: B 215 GLU cc_start: 0.9033 (mp0) cc_final: 0.8476 (mp0) REVERT: B 227 SER cc_start: 0.8958 (t) cc_final: 0.8371 (p) REVERT: C 13 ARG cc_start: 0.9205 (mtt-85) cc_final: 0.9002 (mtm-85) REVERT: C 18 GLN cc_start: 0.8846 (tp40) cc_final: 0.8430 (tp40) REVERT: C 31 SER cc_start: 0.9087 (t) cc_final: 0.8842 (p) REVERT: D 6 GLU cc_start: 0.8066 (mp0) cc_final: 0.7662 (mp0) REVERT: D 67 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8374 (mtm110) REVERT: D 73 ASP cc_start: 0.8597 (t0) cc_final: 0.8141 (t0) REVERT: D 87 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8001 (ttm-80) REVERT: D 128 MET cc_start: 0.8839 (mmm) cc_final: 0.8287 (mmm) REVERT: D 206 ARG cc_start: 0.8681 (ptp-110) cc_final: 0.8471 (ttp80) REVERT: D 219 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.7823 (pp30) outliers start: 52 outliers final: 23 residues processed: 241 average time/residue: 0.1198 time to fit residues: 38.6165 Evaluate side-chains 199 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 0.0070 chunk 81 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN R 350 ASN A 204 GLN A 346 ASN C 24 ASN D 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.068089 restraints weight = 19907.641| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.93 r_work: 0.2754 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10397 Z= 0.134 Angle : 0.634 8.238 14098 Z= 0.331 Chirality : 0.043 0.237 1598 Planarity : 0.004 0.058 1785 Dihedral : 8.959 127.387 1458 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.12 % Allowed : 22.14 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1285 helix: 1.48 (0.24), residues: 487 sheet: -0.72 (0.31), residues: 262 loop : -1.28 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 100 TYR 0.015 0.001 TYR R 339 PHE 0.013 0.001 PHE A 336 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10394) covalent geometry : angle 0.63273 / 0.33 (14092) SS BOND : bond 0.00797 / 0.56 ( 3) SS BOND : angle 2.11818 / 1.73 ( 6) hydrogen bonds : bond 0.04843 / 3.35 ( 504) hydrogen bonds : angle 5.06854 / 3.74 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 55 ASP cc_start: 0.8685 (m-30) cc_final: 0.8154 (m-30) REVERT: R 59 ASP cc_start: 0.7394 (t0) cc_final: 0.6935 (t70) REVERT: R 63 LYS cc_start: 0.9297 (mtmm) cc_final: 0.9053 (mtmt) REVERT: R 94 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8552 (mt) REVERT: R 120 MET cc_start: 0.8258 (ttp) cc_final: 0.7996 (tpp) REVERT: R 134 TRP cc_start: 0.8389 (t-100) cc_final: 0.7021 (t-100) REVERT: R 171 CYS cc_start: 0.8880 (m) cc_final: 0.8561 (m) REVERT: R 210 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7548 (tp40) REVERT: R 262 LYS cc_start: 0.7957 (tppt) cc_final: 0.7669 (tptp) REVERT: R 340 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.8927 (p0) REVERT: A 67 LYS cc_start: 0.9409 (mtmt) cc_final: 0.8995 (ptpt) REVERT: A 88 MET cc_start: 0.8544 (ttt) cc_final: 0.8196 (ptm) REVERT: A 119 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7857 (tpt) REVERT: A 197 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8163 (ptpt) REVERT: A 321 THR cc_start: 0.9374 (m) cc_final: 0.8925 (p) REVERT: A 324 THR cc_start: 0.9235 (m) cc_final: 0.8956 (p) REVERT: B 9 GLN cc_start: 0.9350 (pp30) cc_final: 0.9128 (pp30) REVERT: B 10 GLU cc_start: 0.9440 (tt0) cc_final: 0.8968 (mp0) REVERT: B 59 TYR cc_start: 0.9085 (m-80) cc_final: 0.8473 (m-80) REVERT: B 172 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8396 (tm-30) REVERT: B 188 MET cc_start: 0.8894 (mmm) cc_final: 0.8633 (mmm) REVERT: B 189 SER cc_start: 0.9126 (t) cc_final: 0.8759 (m) REVERT: B 227 SER cc_start: 0.8988 (t) cc_final: 0.8380 (p) REVERT: C 18 GLN cc_start: 0.8621 (tp40) cc_final: 0.8227 (tp40) REVERT: C 31 SER cc_start: 0.9097 (t) cc_final: 0.8861 (p) REVERT: C 58 GLU cc_start: 0.9310 (mt-10) cc_final: 0.9058 (mp0) REVERT: D 6 GLU cc_start: 0.8141 (mp0) cc_final: 0.7529 (mp0) REVERT: D 46 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8129 (mt-10) REVERT: D 73 ASP cc_start: 0.8745 (t0) cc_final: 0.8387 (t70) REVERT: D 87 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8305 (ttm-80) REVERT: D 219 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8659 (pp30) outliers start: 45 outliers final: 20 residues processed: 213 average time/residue: 0.1031 time to fit residues: 29.5481 Evaluate side-chains 197 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 104 optimal weight: 0.0980 chunk 109 optimal weight: 7.9990 chunk 55 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 340 ASN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.063726 restraints weight = 20184.468| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.92 r_work: 0.2665 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10397 Z= 0.229 Angle : 0.650 8.605 14098 Z= 0.340 Chirality : 0.045 0.229 1598 Planarity : 0.004 0.055 1785 Dihedral : 8.297 120.356 1445 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.94 % Allowed : 22.05 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1285 helix: 1.60 (0.24), residues: 487 sheet: -0.59 (0.32), residues: 263 loop : -1.10 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 18 TYR 0.016 0.002 TYR A 167 PHE 0.015 0.002 PHE R 353 TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (10394) covalent geometry : angle 0.64740 / 0.34 (14092) SS BOND : bond 0.01490 / 1.06 ( 3) SS BOND : angle 2.92479 / 2.54 ( 6) hydrogen bonds : bond 0.04826 / 3.33 ( 504) hydrogen bonds : angle 4.95912 / 3.66 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 55 ASP cc_start: 0.8699 (m-30) cc_final: 0.8165 (m-30) REVERT: R 59 ASP cc_start: 0.7657 (t0) cc_final: 0.7132 (t0) REVERT: R 63 LYS cc_start: 0.9330 (mtmm) cc_final: 0.8974 (mtmt) REVERT: R 94 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8553 (mt) REVERT: R 120 MET cc_start: 0.8212 (ttp) cc_final: 0.7954 (tpp) REVERT: R 134 TRP cc_start: 0.8419 (t-100) cc_final: 0.6992 (t-100) REVERT: R 171 CYS cc_start: 0.8918 (m) cc_final: 0.8545 (m) REVERT: R 187 LYS cc_start: 0.8593 (mtpm) cc_final: 0.8257 (tmtt) REVERT: R 262 LYS cc_start: 0.7958 (tppt) cc_final: 0.7667 (tptp) REVERT: R 340 ASP cc_start: 0.9282 (OUTLIER) cc_final: 0.8939 (p0) REVERT: R 346 TYR cc_start: 0.7167 (t80) cc_final: 0.6940 (t80) REVERT: A 25 GLU cc_start: 0.8829 (tt0) cc_final: 0.8116 (tm-30) REVERT: A 67 LYS cc_start: 0.9455 (mtmt) cc_final: 0.9164 (mttt) REVERT: A 108 PHE cc_start: 0.9253 (m-80) cc_final: 0.8807 (m-80) REVERT: A 142 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8700 (mtm-85) REVERT: A 197 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8303 (ptpt) REVERT: A 349 LYS cc_start: 0.8950 (mmtp) cc_final: 0.8587 (mmtm) REVERT: B 227 SER cc_start: 0.9100 (t) cc_final: 0.8442 (p) REVERT: B 300 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9073 (mt) REVERT: C 22 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8760 (mt-10) REVERT: C 24 ASN cc_start: 0.9297 (m-40) cc_final: 0.9080 (m-40) REVERT: C 58 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9025 (mp0) REVERT: D 6 GLU cc_start: 0.8392 (mp0) cc_final: 0.7542 (mp0) REVERT: D 46 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8399 (mt-10) REVERT: D 73 ASP cc_start: 0.8878 (t0) cc_final: 0.8591 (t70) REVERT: D 89 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8455 (pt0) REVERT: D 219 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8201 (pp30) outliers start: 54 outliers final: 29 residues processed: 207 average time/residue: 0.1076 time to fit residues: 29.7309 Evaluate side-chains 199 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN A 141 ASN A 213 HIS B 36 ASN B 340 ASN D 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.063924 restraints weight = 20077.214| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.92 r_work: 0.2669 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10397 Z= 0.201 Angle : 0.631 11.598 14098 Z= 0.330 Chirality : 0.044 0.266 1598 Planarity : 0.004 0.051 1785 Dihedral : 8.019 111.759 1444 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.31 % Allowed : 22.14 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1285 helix: 1.63 (0.24), residues: 490 sheet: -0.51 (0.32), residues: 263 loop : -1.02 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 90 TYR 0.019 0.001 TYR A 167 PHE 0.019 0.001 PHE D 165 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (10394) covalent geometry : angle 0.62890 / 0.33 (14092) SS BOND : bond 0.01321 / 0.94 ( 3) SS BOND : angle 2.50350 / 2.15 ( 6) hydrogen bonds : bond 0.04679 / 3.21 ( 504) hydrogen bonds : angle 4.89602 / 3.62 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 55 ASP cc_start: 0.8722 (m-30) cc_final: 0.8172 (m-30) REVERT: R 59 ASP cc_start: 0.7687 (t0) cc_final: 0.7077 (t70) REVERT: R 63 LYS cc_start: 0.9267 (mtmm) cc_final: 0.8987 (mtpt) REVERT: R 94 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8585 (mt) REVERT: R 120 MET cc_start: 0.8324 (ttp) cc_final: 0.8048 (tpp) REVERT: R 134 TRP cc_start: 0.8451 (t-100) cc_final: 0.7174 (t-100) REVERT: R 171 CYS cc_start: 0.8975 (m) cc_final: 0.8648 (m) REVERT: R 187 LYS cc_start: 0.8603 (mtpm) cc_final: 0.8255 (tmtt) REVERT: R 203 MET cc_start: 0.7578 (tpp) cc_final: 0.7338 (tpp) REVERT: R 210 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7327 (tp40) REVERT: R 262 LYS cc_start: 0.7961 (tppt) cc_final: 0.7686 (tptp) REVERT: R 340 ASP cc_start: 0.9298 (OUTLIER) cc_final: 0.8852 (p0) REVERT: R 346 TYR cc_start: 0.7192 (t80) cc_final: 0.6954 (t80) REVERT: A 25 GLU cc_start: 0.8832 (tt0) cc_final: 0.8116 (tm-30) REVERT: A 67 LYS cc_start: 0.9467 (mtmt) cc_final: 0.9148 (mttt) REVERT: A 88 MET cc_start: 0.8501 (ptm) cc_final: 0.8213 (ptm) REVERT: A 108 PHE cc_start: 0.9249 (m-80) cc_final: 0.8755 (m-80) REVERT: A 119 MET cc_start: 0.8176 (mmm) cc_final: 0.7870 (tpt) REVERT: A 197 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8282 (ptpt) REVERT: A 349 LYS cc_start: 0.8895 (mmtp) cc_final: 0.8543 (mmtt) REVERT: B 59 TYR cc_start: 0.9142 (m-80) cc_final: 0.8707 (m-80) REVERT: B 227 SER cc_start: 0.9129 (t) cc_final: 0.8473 (p) REVERT: B 300 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9136 (mt) REVERT: C 24 ASN cc_start: 0.9343 (m-40) cc_final: 0.9084 (m110) REVERT: C 58 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9005 (mp0) REVERT: D 6 GLU cc_start: 0.8231 (mp0) cc_final: 0.7636 (mp0) REVERT: D 46 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8278 (tt0) REVERT: D 73 ASP cc_start: 0.8890 (t0) cc_final: 0.8619 (t70) REVERT: D 89 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8462 (pt0) REVERT: D 167 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: D 219 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8846 (pp30) outliers start: 58 outliers final: 35 residues processed: 214 average time/residue: 0.1020 time to fit residues: 29.7758 Evaluate side-chains 204 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 40.0000 chunk 65 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN A 149 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.064604 restraints weight = 20270.122| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.93 r_work: 0.2685 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10397 Z= 0.159 Angle : 0.602 8.116 14098 Z= 0.314 Chirality : 0.042 0.226 1598 Planarity : 0.003 0.045 1785 Dihedral : 7.539 108.299 1440 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 4.76 % Allowed : 22.23 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.24), residues: 1285 helix: 1.73 (0.24), residues: 490 sheet: -0.43 (0.32), residues: 258 loop : -0.98 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 206 TYR 0.017 0.001 TYR L 11 PHE 0.014 0.001 PHE D 165 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10394) covalent geometry : angle 0.59905 / 0.31 (14092) SS BOND : bond 0.01257 / 0.89 ( 3) SS BOND : angle 3.00237 / 2.58 ( 6) hydrogen bonds : bond 0.04444 / 3.05 ( 504) hydrogen bonds : angle 4.80127 / 3.56 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 59 ASP cc_start: 0.7702 (t0) cc_final: 0.7080 (t70) REVERT: R 63 LYS cc_start: 0.9296 (mtmm) cc_final: 0.8968 (mtpt) REVERT: R 94 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8656 (mt) REVERT: R 120 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8034 (tpp) REVERT: R 134 TRP cc_start: 0.8469 (t-100) cc_final: 0.7134 (t-100) REVERT: R 171 CYS cc_start: 0.8975 (m) cc_final: 0.8653 (m) REVERT: R 187 LYS cc_start: 0.8664 (mtpm) cc_final: 0.8271 (tmtt) REVERT: R 210 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7313 (tp40) REVERT: R 262 LYS cc_start: 0.7943 (tppt) cc_final: 0.7629 (tptp) REVERT: R 296 GLN cc_start: 0.8442 (tp40) cc_final: 0.8205 (mm-40) REVERT: R 340 ASP cc_start: 0.9299 (OUTLIER) cc_final: 0.8821 (p0) REVERT: R 346 TYR cc_start: 0.7116 (t80) cc_final: 0.6809 (t80) REVERT: R 365 ASN cc_start: 0.8070 (t0) cc_final: 0.7690 (t0) REVERT: A 25 GLU cc_start: 0.8836 (tt0) cc_final: 0.8122 (tm-30) REVERT: A 67 LYS cc_start: 0.9486 (mtmt) cc_final: 0.9151 (mttt) REVERT: A 88 MET cc_start: 0.8339 (ptm) cc_final: 0.8050 (ptm) REVERT: A 108 PHE cc_start: 0.9254 (m-80) cc_final: 0.8747 (m-80) REVERT: A 197 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8280 (ptpt) REVERT: A 328 ASP cc_start: 0.9211 (t0) cc_final: 0.8587 (t0) REVERT: A 349 LYS cc_start: 0.8880 (mmtp) cc_final: 0.8534 (mmtt) REVERT: B 59 TYR cc_start: 0.9079 (m-80) cc_final: 0.8646 (m-80) REVERT: B 172 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8614 (tm-30) REVERT: B 227 SER cc_start: 0.9131 (t) cc_final: 0.8466 (p) REVERT: C 13 ARG cc_start: 0.9167 (mtm-85) cc_final: 0.8962 (mtt-85) REVERT: C 24 ASN cc_start: 0.9355 (m-40) cc_final: 0.9059 (m110) REVERT: C 58 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8998 (mp0) REVERT: D 6 GLU cc_start: 0.8155 (mp0) cc_final: 0.7560 (mp0) REVERT: D 46 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8393 (tt0) REVERT: D 73 ASP cc_start: 0.8888 (t0) cc_final: 0.8627 (t70) REVERT: D 89 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8421 (pt0) REVERT: D 167 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: D 206 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7445 (ttp80) REVERT: D 219 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8963 (pp30) outliers start: 52 outliers final: 32 residues processed: 209 average time/residue: 0.1010 time to fit residues: 28.6642 Evaluate side-chains 206 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 98 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064904 restraints weight = 20153.625| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.92 r_work: 0.2693 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10397 Z= 0.153 Angle : 0.615 10.391 14098 Z= 0.316 Chirality : 0.043 0.322 1598 Planarity : 0.003 0.038 1785 Dihedral : 7.273 107.592 1436 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 4.57 % Allowed : 22.42 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1285 helix: 1.71 (0.24), residues: 492 sheet: -0.38 (0.32), residues: 258 loop : -0.95 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 18 TYR 0.018 0.001 TYR A 167 PHE 0.012 0.001 PHE D 165 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10394) covalent geometry : angle 0.61252 / 0.31 (14092) SS BOND : bond 0.01219 / 0.87 ( 3) SS BOND : angle 2.72004 / 2.34 ( 6) hydrogen bonds : bond 0.04338 / 2.98 ( 504) hydrogen bonds : angle 4.80150 / 3.58 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 59 ASP cc_start: 0.7704 (t0) cc_final: 0.7171 (t0) REVERT: R 63 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8949 (mtpt) REVERT: R 94 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8660 (mt) REVERT: R 120 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8045 (tpp) REVERT: R 134 TRP cc_start: 0.8507 (t-100) cc_final: 0.7187 (t-100) REVERT: R 171 CYS cc_start: 0.8948 (m) cc_final: 0.8578 (m) REVERT: R 187 LYS cc_start: 0.8666 (mtpm) cc_final: 0.8266 (tmtt) REVERT: R 203 MET cc_start: 0.7498 (tpp) cc_final: 0.7245 (tpp) REVERT: R 210 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7360 (tp40) REVERT: R 262 LYS cc_start: 0.7946 (tppt) cc_final: 0.7635 (tptp) REVERT: R 296 GLN cc_start: 0.8483 (tp40) cc_final: 0.8251 (mm-40) REVERT: R 340 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.8801 (p0) REVERT: R 346 TYR cc_start: 0.7126 (t80) cc_final: 0.6777 (t80) REVERT: R 365 ASN cc_start: 0.7929 (t0) cc_final: 0.7569 (t0) REVERT: A 67 LYS cc_start: 0.9457 (mtmt) cc_final: 0.9107 (mttt) REVERT: A 88 MET cc_start: 0.8323 (ptm) cc_final: 0.8005 (ptm) REVERT: A 108 PHE cc_start: 0.9240 (m-80) cc_final: 0.8729 (m-80) REVERT: A 128 LYS cc_start: 0.9705 (mmtt) cc_final: 0.9224 (mmmt) REVERT: A 197 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8283 (ptpt) REVERT: A 240 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7190 (pmm) REVERT: A 328 ASP cc_start: 0.9232 (t0) cc_final: 0.8624 (t0) REVERT: A 349 LYS cc_start: 0.8887 (mmtp) cc_final: 0.8535 (mmtt) REVERT: B 4 LEU cc_start: 0.9131 (tt) cc_final: 0.8756 (tt) REVERT: B 8 ARG cc_start: 0.9121 (ttm110) cc_final: 0.8714 (mpt-90) REVERT: B 59 TYR cc_start: 0.9076 (m-80) cc_final: 0.8631 (m-80) REVERT: B 172 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8904 (tp30) REVERT: B 227 SER cc_start: 0.9138 (t) cc_final: 0.8471 (p) REVERT: C 13 ARG cc_start: 0.9145 (mtm-85) cc_final: 0.8915 (mtt-85) REVERT: C 58 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8988 (mp0) REVERT: D 6 GLU cc_start: 0.8130 (mp0) cc_final: 0.7784 (mp0) REVERT: D 46 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8476 (tt0) REVERT: D 73 ASP cc_start: 0.8981 (t0) cc_final: 0.8749 (t70) REVERT: D 89 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8422 (pt0) REVERT: D 167 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.7942 (tm-30) outliers start: 50 outliers final: 35 residues processed: 210 average time/residue: 0.1113 time to fit residues: 31.5867 Evaluate side-chains 210 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 67 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN B 340 ASN C 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.063387 restraints weight = 20183.878| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.91 r_work: 0.2670 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10397 Z= 0.212 Angle : 0.639 8.874 14098 Z= 0.330 Chirality : 0.043 0.230 1598 Planarity : 0.004 0.031 1785 Dihedral : 7.196 110.887 1436 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 4.39 % Allowed : 22.87 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1285 helix: 1.69 (0.24), residues: 492 sheet: -0.42 (0.31), residues: 276 loop : -0.90 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 206 TYR 0.020 0.001 TYR A 167 PHE 0.012 0.001 PHE D 165 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (10394) covalent geometry : angle 0.63564 / 0.33 (14092) SS BOND : bond 0.01444 / 1.03 ( 3) SS BOND : angle 3.00048 / 2.56 ( 6) hydrogen bonds : bond 0.04527 / 3.10 ( 504) hydrogen bonds : angle 4.82030 / 3.58 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 59 ASP cc_start: 0.7729 (t0) cc_final: 0.7067 (t70) REVERT: R 63 LYS cc_start: 0.9264 (mtmm) cc_final: 0.8993 (mtpt) REVERT: R 94 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8660 (mt) REVERT: R 120 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7935 (tpp) REVERT: R 134 TRP cc_start: 0.8529 (t-100) cc_final: 0.7238 (t-100) REVERT: R 171 CYS cc_start: 0.8981 (m) cc_final: 0.8640 (m) REVERT: R 187 LYS cc_start: 0.8720 (mtpm) cc_final: 0.8293 (tmtt) REVERT: R 203 MET cc_start: 0.7528 (tpp) cc_final: 0.7285 (tpp) REVERT: R 210 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7402 (tm-30) REVERT: R 262 LYS cc_start: 0.7979 (tppt) cc_final: 0.7661 (tptp) REVERT: R 294 ARG cc_start: 0.8597 (mtt180) cc_final: 0.8366 (mtt180) REVERT: R 340 ASP cc_start: 0.9326 (OUTLIER) cc_final: 0.8824 (p0) REVERT: R 346 TYR cc_start: 0.7273 (t80) cc_final: 0.6966 (t80) REVERT: R 365 ASN cc_start: 0.8145 (t0) cc_final: 0.7736 (t0) REVERT: A 25 GLU cc_start: 0.8834 (tt0) cc_final: 0.8121 (tm-30) REVERT: A 67 LYS cc_start: 0.9476 (mtmt) cc_final: 0.9123 (mttt) REVERT: A 88 MET cc_start: 0.8356 (ptm) cc_final: 0.7989 (ptm) REVERT: A 95 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8181 (t80) REVERT: A 108 PHE cc_start: 0.9243 (m-80) cc_final: 0.8707 (m-80) REVERT: A 128 LYS cc_start: 0.9721 (mmtt) cc_final: 0.9433 (mmtt) REVERT: A 240 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7740 (pmm) REVERT: A 328 ASP cc_start: 0.9233 (t0) cc_final: 0.8600 (t0) REVERT: A 349 LYS cc_start: 0.8895 (mmtp) cc_final: 0.8594 (mmtt) REVERT: B 10 GLU cc_start: 0.9383 (tt0) cc_final: 0.9138 (tp30) REVERT: B 172 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8879 (tp30) REVERT: B 227 SER cc_start: 0.9147 (t) cc_final: 0.8470 (p) REVERT: C 58 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8972 (mp0) REVERT: D 6 GLU cc_start: 0.8242 (mp0) cc_final: 0.7557 (mp0) REVERT: D 46 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: D 73 ASP cc_start: 0.8954 (t0) cc_final: 0.8709 (t70) REVERT: D 89 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8284 (pt0) REVERT: D 167 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: D 206 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7511 (ttp80) outliers start: 48 outliers final: 30 residues processed: 204 average time/residue: 0.1166 time to fit residues: 32.1682 Evaluate side-chains 203 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 40.0000 chunk 31 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.064144 restraints weight = 20141.668| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.91 r_work: 0.2679 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10397 Z= 0.178 Angle : 0.638 10.858 14098 Z= 0.330 Chirality : 0.044 0.386 1598 Planarity : 0.003 0.033 1785 Dihedral : 7.015 110.180 1436 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 3.57 % Allowed : 24.34 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1285 helix: 1.75 (0.24), residues: 492 sheet: -0.40 (0.31), residues: 274 loop : -0.89 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 206 TYR 0.018 0.001 TYR A 167 PHE 0.013 0.001 PHE D 165 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10394) covalent geometry : angle 0.63584 / 0.33 (14092) SS BOND : bond 0.01284 / 0.91 ( 3) SS BOND : angle 2.64779 / 2.26 ( 6) hydrogen bonds : bond 0.04421 / 3.05 ( 504) hydrogen bonds : angle 4.76946 / 3.54 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 59 ASP cc_start: 0.7740 (t0) cc_final: 0.7067 (t70) REVERT: R 63 LYS cc_start: 0.9259 (mtmm) cc_final: 0.8968 (mtpt) REVERT: R 94 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8678 (mt) REVERT: R 112 ASP cc_start: 0.8701 (m-30) cc_final: 0.8203 (t0) REVERT: R 120 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7922 (tpp) REVERT: R 134 TRP cc_start: 0.8553 (t-100) cc_final: 0.7152 (t-100) REVERT: R 171 CYS cc_start: 0.8963 (m) cc_final: 0.8595 (m) REVERT: R 187 LYS cc_start: 0.8691 (mtpm) cc_final: 0.8257 (tmtt) REVERT: R 203 MET cc_start: 0.7471 (tpp) cc_final: 0.7217 (tpp) REVERT: R 210 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7451 (tm-30) REVERT: R 262 LYS cc_start: 0.7976 (tppt) cc_final: 0.7664 (tptp) REVERT: R 340 ASP cc_start: 0.9331 (OUTLIER) cc_final: 0.8810 (p0) REVERT: R 346 TYR cc_start: 0.7318 (t80) cc_final: 0.6975 (t80) REVERT: R 365 ASN cc_start: 0.8007 (t0) cc_final: 0.7617 (t0) REVERT: A 25 GLU cc_start: 0.8832 (tt0) cc_final: 0.8118 (tm-30) REVERT: A 67 LYS cc_start: 0.9493 (mtmt) cc_final: 0.9158 (mttt) REVERT: A 88 MET cc_start: 0.8337 (ptm) cc_final: 0.7983 (ptm) REVERT: A 95 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8208 (t80) REVERT: A 108 PHE cc_start: 0.9334 (m-80) cc_final: 0.8794 (m-80) REVERT: A 128 LYS cc_start: 0.9707 (mmtt) cc_final: 0.9327 (mmmt) REVERT: A 328 ASP cc_start: 0.9208 (t0) cc_final: 0.8572 (t0) REVERT: A 349 LYS cc_start: 0.8881 (mmtp) cc_final: 0.8565 (mmtt) REVERT: B 10 GLU cc_start: 0.9411 (tt0) cc_final: 0.9166 (tp30) REVERT: B 227 SER cc_start: 0.9158 (t) cc_final: 0.8488 (p) REVERT: C 20 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8447 (ptpp) REVERT: C 58 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8968 (mp0) REVERT: D 6 GLU cc_start: 0.8150 (mp0) cc_final: 0.7469 (mp0) REVERT: D 46 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: D 73 ASP cc_start: 0.8937 (t0) cc_final: 0.8694 (t70) REVERT: D 89 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8289 (pt0) REVERT: D 167 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.7938 (tm-30) outliers start: 39 outliers final: 30 residues processed: 194 average time/residue: 0.1133 time to fit residues: 29.7520 Evaluate side-chains 201 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 127 optimal weight: 0.0770 chunk 48 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 30.0000 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN B 239 ASN C 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.066067 restraints weight = 19905.899| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.92 r_work: 0.2725 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10397 Z= 0.132 Angle : 0.628 13.891 14098 Z= 0.321 Chirality : 0.043 0.384 1598 Planarity : 0.003 0.032 1785 Dihedral : 6.728 103.867 1435 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.02 % Allowed : 24.34 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1285 helix: 1.83 (0.24), residues: 494 sheet: -0.23 (0.32), residues: 261 loop : -0.87 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 105 TYR 0.016 0.001 TYR L 11 PHE 0.012 0.001 PHE D 165 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10394) covalent geometry : angle 0.62649 / 0.32 (14092) SS BOND : bond 0.01003 / 0.71 ( 3) SS BOND : angle 2.20325 / 1.89 ( 6) hydrogen bonds : bond 0.04134 / 2.83 ( 504) hydrogen bonds : angle 4.68636 / 3.48 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 59 ASP cc_start: 0.7710 (t0) cc_final: 0.7044 (t70) REVERT: R 63 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8977 (mtpt) REVERT: R 94 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8674 (mt) REVERT: R 112 ASP cc_start: 0.8582 (m-30) cc_final: 0.8090 (t0) REVERT: R 120 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7916 (tpp) REVERT: R 134 TRP cc_start: 0.8500 (t-100) cc_final: 0.7118 (t-100) REVERT: R 171 CYS cc_start: 0.8922 (m) cc_final: 0.8596 (m) REVERT: R 187 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8256 (tmtt) REVERT: R 203 MET cc_start: 0.7468 (tpp) cc_final: 0.7155 (tpp) REVERT: R 210 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7538 (tm-30) REVERT: R 262 LYS cc_start: 0.7977 (tppt) cc_final: 0.7713 (tptp) REVERT: R 294 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8308 (mtt180) REVERT: R 333 GLN cc_start: 0.7849 (tt0) cc_final: 0.7542 (mt0) REVERT: R 340 ASP cc_start: 0.9315 (OUTLIER) cc_final: 0.8769 (p0) REVERT: R 346 TYR cc_start: 0.7209 (t80) cc_final: 0.6779 (t80) REVERT: A 25 GLU cc_start: 0.8820 (tt0) cc_final: 0.8119 (tm-30) REVERT: A 67 LYS cc_start: 0.9515 (mtmt) cc_final: 0.9184 (mttt) REVERT: A 88 MET cc_start: 0.8325 (ptm) cc_final: 0.7998 (ptm) REVERT: A 102 ASP cc_start: 0.9512 (m-30) cc_final: 0.9291 (m-30) REVERT: A 328 ASP cc_start: 0.9185 (t0) cc_final: 0.8610 (t0) REVERT: A 330 LYS cc_start: 0.9421 (mtmm) cc_final: 0.9132 (mmmt) REVERT: A 349 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8613 (mmtt) REVERT: B 8 ARG cc_start: 0.9219 (ttm110) cc_final: 0.8705 (mtm-85) REVERT: B 227 SER cc_start: 0.9149 (t) cc_final: 0.8513 (p) REVERT: B 262 MET cc_start: 0.8932 (tpp) cc_final: 0.8218 (ttm) REVERT: C 21 MET cc_start: 0.9596 (tpp) cc_final: 0.9377 (mmm) REVERT: C 58 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8950 (mp0) REVERT: D 46 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: D 73 ASP cc_start: 0.8919 (t0) cc_final: 0.8595 (t70) REVERT: D 89 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8309 (pt0) REVERT: D 128 MET cc_start: 0.9004 (mmm) cc_final: 0.8431 (mmm) REVERT: D 167 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: D 206 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7898 (tmm-80) REVERT: D 232 LYS cc_start: 0.8707 (tttt) cc_final: 0.8488 (tttm) outliers start: 33 outliers final: 25 residues processed: 199 average time/residue: 0.1092 time to fit residues: 29.5213 Evaluate side-chains 193 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN B 36 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.094166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.061749 restraints weight = 20649.268| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.99 r_work: 0.2624 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10397 Z= 0.312 Angle : 0.728 12.689 14098 Z= 0.378 Chirality : 0.048 0.361 1598 Planarity : 0.004 0.039 1785 Dihedral : 7.043 108.120 1435 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.29 % Allowed : 24.15 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1285 helix: 1.62 (0.24), residues: 495 sheet: -0.41 (0.31), residues: 284 loop : -0.83 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 105 TYR 0.020 0.002 TYR L 11 PHE 0.017 0.002 PHE R 353 TRP 0.025 0.002 TRP A 131 HIS 0.006 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.31 (10394) covalent geometry : angle 0.72488 / 0.38 (14092) SS BOND : bond 0.01838 / 1.31 ( 3) SS BOND : angle 3.46426 / 2.92 ( 6) hydrogen bonds : bond 0.04811 / 3.29 ( 504) hydrogen bonds : angle 4.92479 / 3.65 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.76 seconds wall clock time: 39 minutes 48.88 seconds (2388.88 seconds total)